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The discoloration is only a surface oxide. It is removed in the post-HT grinding and finishing.
If it is deeper than that you may have a foil pouch not sealed properly.
You will find suggestions with putting a piece of paper or charcoal in the pouch. This is not done much anymore. It really doesn't do much. Double sealing the seams and rolling or hammering them tight with a wooden or nylon mallet works best.
There is a tendency for new knifemakers to think that the blade comes out of HT ready for a handle and sharpening. This is not true. The surface of the blade needs to be sanded down at least .005" to remove the "skin" of carbon depleted metal. It can be deeper than that in some cases. Many makers doing stainless steels now only profile the blade and then do HT. The bevels and plunge are ground after HT. A water mist system like the Kool-Mist setup is very helpful here, but you can do it by the grind-and-dip method.
Tell us about what steel you are using, your HT method details, and maybe post a photo of the discoloration you are referring to. That will help us determine what the issue is.